Modeling chemical reactions in classical molecular dynamics simulations

JR Gissinger and BD Jensen and KE Wise, POLYMER, 128, 211-217 (2017).

DOI: 10.1016/j.polymer.2017.09.038

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post- reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly- crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed. Published by Elsevier Ltd.

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